I haven't played too may to be perfectly honest, but I thought the Bleach Heat the Soul games were pretty fun. It had most of the main characters and had some pretty neat combos you could do and they fighting styles of each character matched their anime forms, which was great.
It's not based on an anime per se, but Jump Ultimate Stars is a great Smash Bros. -esque crossover fighting game featuring a huge selection of Shonen Jump titles. In a way, it settles all those debates of "Who would win it a fight: Goku, Naruto, or Luffy?" in a fun fighting format.